Genetic Variant NM_001074.4:c.1311-107G>A (chr4-69112350-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001074.4(UGT2B7):c.1311-107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 1,428,130 control chromosomes in the GnomAD database, including 184,918 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.59 ( 27550 hom., cov: 32)

Exomes 𝑓: 0.49 ( 157368 hom. )

Consequence

UGT2B7
NM_001074.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.220

Publications

3 publications found

Variant links:

Genes affected

UGT2B7 (HGNC:12554): (UDP glucuronosyltransferase family 2 member B7) The protein encoded by this gene belongs to the UDP-glycosyltransferase (UGT) family. UGTs serve a major role in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This protein is localized in the microsome membrane, and has unique specificity for 3,4-catechol estrogens and estriol, suggesting that it may play an important role in regulating the level and activity of these potent estrogen metabolites. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2017]

UGT2B7 links:

ENSG00000299782 (HGNC:):

ENSG00000299782 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
UGT2B7	NM_001074.4 link	c.1311-107G>A	intron_variant	Intron 5 of 5	ENST00000305231.12	NP_001065.2	P16662
UGT2B7	NM_001330719.2 link	c.1091-107G>A	intron_variant	Intron 4 of 4		NP_001317648.1	P16662E9PBP8
UGT2B7	NM_001349568.2 link	c.564-107G>A	intron_variant	Intron 6 of 6		NP_001336497.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT2B7	ENST00000305231.12 link	c.1311-107G>A		intron_variant	Intron 5 of 5	1	NM_001074.4	ENSP00000304811.7		P16662

Frequencies

GnomAD3 genomes

AF:

0.588

AC:

89317

AN:

151828

Hom.:

27502

Cov.:

show subpopulations

Gnomad AFR

AF:

0.751

Gnomad AMI

AF:

0.489

Gnomad AMR

AF:

0.666

Gnomad ASJ

AF:

0.512

Gnomad EAS

AF:

0.705

Gnomad SAS

AF:

0.567

Gnomad FIN

AF:

0.575

Gnomad MID

AF:

0.579

Gnomad NFE

AF:

0.471

Gnomad OTH

AF:

0.601

GnomAD4 exome

AF:

0.490

AC:

625238

AN:

1276184

Hom.:

157368

AF XY:

0.491

AC XY:

307657

AN XY:

627184

show subpopulations

African (AFR)

AF:

0.755

AC:

20934

AN:

27722

American (AMR)

AF:

0.699

AC:

16909

AN:

24186

Ashkenazi Jewish (ASJ)

AF:

0.513

AC:

10018

AN:

19544

East Asian (EAS)

AF:

0.710

AC:

25415

AN:

35808

South Asian (SAS)

AF:

0.529

AC:

34223

AN:

64640

European-Finnish (FIN)

AF:

0.580

AC:

26429

AN:

45548

Middle Eastern (MID)

AF:

0.524

AC:

1872

AN:

3570

European-Non Finnish (NFE)

AF:

0.461

AC:

461935

AN:

1001934

Other (OTH)

AF:

0.517

AC:

27503

AN:

53232

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

15430

30861

46291

61722

77152

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14144

28288

42432

56576

70720

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.589

AC:

89421

AN:

151946

Hom.:

27550

Cov.:

AF XY:

0.597

AC XY:

44313

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.751

AC:

31108

AN:

41420

American (AMR)

AF:

0.667

AC:

10190

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.512

AC:

1778

AN:

3470

East Asian (EAS)

AF:

0.704

AC:

3631

AN:

5158

South Asian (SAS)

AF:

0.567

AC:

2730

AN:

4812

European-Finnish (FIN)

AF:

0.575

AC:

6067

AN:

10550

Middle Eastern (MID)

AF:

0.588

AC:

173

AN:

294

European-Non Finnish (NFE)

AF:

0.471

AC:

32030

AN:

67944

Other (OTH)

AF:

0.602

AC:

1271

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1788

3576

5364

7152

8940

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

730

1460

2190

2920

3650

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.534

Hom.:

2966

Bravo

AF:

0.603

Asia WGS

AF:

0.642

AC:

2230

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.1

(source)

DANN

Benign

0.39

PhyloP100

-0.22

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over